Analysis of DNA-protein interactions in complexes of transcription factor NF-κB with DNA

We have applied bioinformatic analysis of X-ray 3D structures of complexes of transcription factor NF-kappa B with DNAs. We determined the number of possible Van der Waals contacts and hydrogen bonds between amino acid residues and nucleotides. Conservative contacts in the NF-kappa B dimer-DNA complex composed of p50 and/or p65 NF-kappa B subunit and DNA sequences like 5'-GGGAMWTTCC-3' were revealed. Based on these results, we propose a novel scheme for interactions between NF-kappa B p50 homodimer and the kappa B region of the immunoglobulin light chain gene enhancer Ig-kappa B). We applied a chemical cross-linking technique to study the proximity of some Lys and Cys residues of NF-kappa B p50 subunit with certain reactive nucleotides into its recognition site. In all cases, the experimentally determined protein-DNA contacts were in good agreement with the predicted ones.